[miso-users] new annotation

[Yarden Katz]

The alternative exon overlap is much larger.   The whole event (i.e. exon trio) depends on flanking exons, and choosing flanking exons will depend on your annotation, so it's natural that there's some variation across different database versions and different methods of choosing flanking exons.  For example, you can pick the two longest flanking exons or two shortest, etc.   The old annotation (v1) was derived independently (i.e. not by me) in Wang et. al. 2008 using the databases that existed around that time, pooling transcripts and ESTs from AceView, Ensembl, UCSC, etc.  The second annotation excluded AceView.  The new annotation also did not use events that had only possible based on EST support but unannotated in Ensembl/UCSC.

  --Yarden






On Sep 9, 2013, at 7:01 PM, Ronghui Li wrote:

> It is the mouse mm9 annotations. By overlapping, I mean the two events are exactly the same between old and new annotations. I used MISO to analyze the same bam file using both old and new annotations. And a lot of events using old annotations did not show up in the results using new annotation. Then I noticed a lot of old events are not documented in the new annotations. 
> 
> 
> On Mon, Sep 9, 2013 at 5:51 PM, Yarden Katz <yarden at mit.edu> wrote:
> Hi,
> 
> Is this human or mouse annotations that you're using?  Also, how did you define overlap?
> 
>   --Yarden
> 
> 
> 
> On Sep 9, 2013, at 5:52 PM, Ronghui Li wrote:
> 
> > Hi Yarden,
> >
> > I have used both the old and new alternative event annotations for MISO. And I noticed that the old and new annotations do not overlap very much. For SE events, roughly 25% of events overlap between old and new annotations. Now I am confused about which one I should use. Or should I combine all the events in the old and new annotations and create a new comprehensive list?
> >
> > --
> > Best regards!
> >
> > Ronghui Li
> > Cellular and Molecular Biology Program
> > Waisman Center
> > University of Wisconsin-Madison
> >
> > _______________________________________________
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> > miso-users at mit.edu
> > http://mailman.mit.edu/mailman/listinfo/miso-users
> 
> 
> 
> 
> -- 
> Best regards!
> 
> Ronghui Li
> Cellular and Molecular Biology Program
> Waisman Center
> University of Wisconsin-Madison
>